Applying molecular tools for improving livestock performance: From DNA markers to next generation sequencing technologies

In the last 25 years, DNA markers and associated molecular techniques have created new possibilities for genetic improvement, conservation of biodiversity, and imparting disease resistance in plants and animals, which led to better standard operating procedures for further targeted breeding. The discovery of the PCR had a major influence on genome analyses and contributed towards the development and application of various DNA markers. The need of the hour is to conserve the genetic resources of animals and therefore, the use of DNA marker technology has become popular among the animal geneticists and breeders. In the last 15 years, advancement in molecular marker techniques have played a significant role in animal genetic improvement strategies and have been incorporated into strains protection laws. Molecular markers are indispensable tools for determining the genetic variation and biodiversity with high levels of accuracy and reproducibility. These markers are mainly classified into two types, the widely used mitochondrial DNA markers with decreasing order of conserved sequences and the most commonly used nuclear markers for DNA fingerprinting include random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and microsatellites. This article overviews molecular DNA markers such as SSR, SNP, RFLP, AFLP, microsatellites and other technologies for their applications in functional genomics, strain improvement and domestic animal breeding regime. We will compare these technologies with “Next generation DNA sequencing” to critically examine the futuristic breeding strategies and their promises and pitfalls.